[project]
name = "simplexuq-code"
version = "0.1.0"
requires-python = ">=3.10,<3.14"
dependencies = [
    "numpy>=1.24",
    "scipy>=1.10",
    "scikit-learn>=1.3",
    "matplotlib>=3.7",
    "pyyaml>=6.0",
]

[project.optional-dependencies]
bio = ["scanpy", "anndata", "rpy2"]    # for deconvolution experiments
r = ["rpy2"]                            # for R integration (visualization, scRNA analysis)
dev = ["pytest", "ruff", "ipykernel"]
gpu = ["torch>=2.0", "torchvision>=0.15"]  # for CIFAR softmax experiment

[tool.setuptools.packages.find]
where = ["."]
include = ["src*"]

[tool.ruff]
line-length = 100
select = ["E", "F", "I"]

[tool.pytest.ini_options]
testpaths = ["tests"]